some test code for flag parsing inside its own classes
forgot key files
point build-common to newest version containing scripts for Jenkins integration
Merge branch 'flag_classes' into config
breaking LibInfo into two separate classes. Not yet sure where names go.
replace LibraryInfo with LibraryConfig in BamConfig
further shuffling of code. Likely broken
LibraryConfig at least compiles now
allow BamConfig to at least compile.
switch over to LibraryConfig
rename LibraryAnalyzer
change name of class
add files to CMakeLists and clean up some compile errors
get all new classes compiling. still untested.
Merge branch 'merged' into config
changes to start to hook things up. horrible.
more changes to start to hook things up. even more horrible.
compiling. may not be functional. tests are broken.
fixed some out of bounds errors. tests now pass
partial merge. need to fix new code around SvBuilder